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<h1>Stereo Specification</h1>

<h2> Basic stereo specification </h2>
<ul>
<li> <b>Chirality </b> 
    <p> The relative position of ligands on a chiral atom is marked 
    with wedge bonds: <i>up (solid)</i>, <i>down (hatched)</i>, 
    <i>up or down (wiggly)</i>.
    Having wedge bonds at chiral atoms with the <i>chiral flag</i> on 
    the entire structure implies that a single isomer is present. 
    The absolute configuration (R or S) is known for 
    all chiral centers that are marked with wedge bonds.</p>  
    

    <p> Non-stereo bond to atom at stereogenic centers 
    implies that no information is known about the configuration 
    of a stereogenic center. It could be either of two stereoisomers, 
    or a mixture of the two.</p>

    <p>The existence of wedge bonds at chiral atoms <i>without chiral flag</i>
	on the entire structure has two meanings depending on the file format
	used.<br>
    <a HREF="../formats/mol-csmol-doc.html#mol">MDL file types (mol, sdf ...)</a>:
    The structure is a racemic mixture of the two enantiomers.<br>
    <a HREF="../formats/smiles-doc.html">Daylight file types (smiles, smarts)</a>:
    Wedges mean absolute stereo configuration, the structure represents a
	single enantiomer. 
    
    </li>

<li> <b>Cis-Trans isomerism</b>
    <p> The positions of the double bond ligands already define 
    the stereo configuration of the double bond (<i>cis</i> or <i>trans</i>). 
    Special query double bond types allow us to specify 
    <i>cis or trans</i>, <i>not trans</i> or <i>not cis</i> isomers.
    
    </li>
</ul>


<h2><a class="anchor" name="enhanced">Enhanced stereo specification</a></h2>
<p> Works in MDL molecule formats: mol, rgf, sdf, rxn etc... 
and in ChemAxon Extended SMILES format: cxsmiles.
<p> Enhanced stereochemical representation introduces three types of 
identifiers that can be attached to a stereogenic center. 
A stereochemical group label is composed from an identifier and a group number.
Each stereogenic center marked with wedge bonds belongs to one (and only one) 
stereochemical group. Grouping allows us to specify relative relationships 
among stereogenic centers. </p>

<blockquote>
<h3>Stereochemical group types:</h3>
<ul>
    <li> ABS <br>
    Stereogenic center where the absolute configuration is known.
	</li>
    <li> OR <br>
    Stereogenic center where the relative configuration is known, 
    but the absolute configuration is not known. The structure 
    represents one stereoisomer that is either 
    the structure as drawn (R,S) OR the epimer in which the 
    stereogenic centers have the opposite configuration (S,R).
	</li>
    <li> AND <br>
    Mixture of stereoisomers. It can be a pair of enantiomers 
    or all the diastereomers. 
	</li>
</ul>

</blockquote>


<p>
<h2>References</h2>
<table CELLSPACING=0 CELLPADDING=5 border="0">
<tr VALIGN=TOP>
<td>[1]</td>
<td><a HREF="http://www.mdl.com/downloads/public/ctfile/ctfile.pdf" TARGET="_top">http://www.mdl.com/downloads/public/ctfile/ctfile.pdf</a></td>
</tr>
</table>

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